The Emerald Alliance: Aqua Version
by WriterBaboon
Summary: War is coming. Team Magma and Aqua have rose to power, and the entire world is in the middle of it. The rebellion group known as the Emerald Alliance may be the only hope left for the world.
1. Chapter 1

**Prologue:** _ **Aqua Version**_

The world is changing. Ever since Team Aqua and Team Magma rose to power, people have been forced to take sides. If they didn't, they were banished or dead, some of who joined the rebel group known as the Emerald Alliance. Ex-Team members were quickly crushed under the power of Aqua and Magma, along with aforementioned civilians who didn't choose a side.

Both adults and teens alike joined these criminal organizations and have turned on each other. Team Aqua members are slick and weasel their ways to get what they want. They were never caught and have a strange love for water Pokemon. Those who joined the side of Team Magma are believed to take anything by brute force or power. They work well alone, but even better when in a union. When working together, they can conquer anything.

Currently, Team Magma controls most of the land-based regions, like Kanto, Johto, and parts of Sinnoh. Team Aqua controls most oceans, parts of Sinnoh, most of Hoenn, a small part of Kanto and Johto, and all of Unova. The only region yet to be taken over is the Kalos region, but rumor has it that a takeover is in the works.

A few fights and battles have occurred here and there, but nothing will compare to the bloodshed soon to come. War is coming.

 **Hey guys, WriterBaboon here! As usual, I'm sorry I don't post as much as I like, but this story is different. If you haven't already, check out the Magma Version of the same story, written by Dragon367! No word on when the next upload will be, but hopefully soon!**

 **It's time to change fanfiction writing forever!**

 **Peace ;-)**


	2. Chapter 2

**The Emerald Alliance: Aqua Version**

Chapter One

"Come on, I've got to go. Neptune is expecting us to be at the rally point." A man with long green hair that reached down to his mid-back said as he pulled away from the brunette girl who was clinging to his arm.

"Oh please, N?' The brunette pouted. "Just ten more minutes."

"Hilda you know I can't stay." N said finally getting his arm free. "I have to be early because,"

"Because Commander Uranus told you so," Hilda said cutting him off. "Come on N, stand up to that strict stiff, he's just a big meanie."

"It's Neptune, and just because he's strict doesn't make him mean." N said defending his commander. "He's just….well…"

"Now you know that's a lie." Hilda said leaning back on the red silk queen sized bed. "Remember what kind of person he is, where he came from."

"Yeah and yet you still fell for him too," N said as he put on a long sleeved white shirt. "And what about me? Remember what I did? He said walking over to the changing rack where he found his pants.

"Yeah, but that's not the same." The brunette stated angrily. "Ghetsis tricked you."

"Yes and Neptune's the same way." N said getting dressed. "He was blindly following Cyrus not because he was evil, but because he was loved Cyrus like I loved Ghetsis and would do anything for him."

"Sounds more like a soldier," Hilda said puffing out her cheeks and bringing her legs to her chest.

"He isn't all bad," N said pulling his Plasma emblem necklace over his head.

"Wow, you're so handsome." Hilda gushed changing the conversation.

"Thanks, my sweet angel," he said kneeling down and kissing her forehead. "Don't worry, soon these teams will fall and we can settle down somewhere."

"I'd like that." She said dreamy-eyed.

BANG! BANG! BANG!

"Come on Romeo, Ash is going to kill us if we don't hurry," yelled a feminine voice, known as Mars, from outside of the couple's door.

"I'll be right out!" N yelled out before turning to look into Hilda's blue deep blue eyes. "And I will see you later." He said kissing her one last time before standing up.

"Yeah, yeah, I know." She said rolling her eyes and smirking.

Scene Change – Outside the door

"Where is he?" Mars said impatiently as she angrily tapped her foot on the ground. "They're moving slower than Slugma in there."

"Come on Rose, The Blue-Haired trainer known as Saturn said. "Give him a break, these are the last few days N and Hilda can spend time together, they won't be seeing each other for a long time. You were the same with Ash before he got shipped off to Jane for training…er….well except you guys didn't have,"

"Ah shut up!" Mars said punching his arm. "And that's Mars to you."

"Ow! That hurt!" Saturn said cradling his now bruised arm.

"Man up, Saturn." N said opening his door.

"Oh you're finally up." The red-head said clearly annoyed. "Come on let's go."

The trio walked into the headquarters, more like living room of the team they were paired up with. The room was made of rich brown spruce wood that covered the floor, ceiling and walls, except for the corner in the far right of the room where the kitchen was set up. To their right a television that was in the middle of three couches that were spread in a 'U' formation. The couch on the left of the group of couches was a three man, the middle was a big couch that curved and it could fit about nine people on it. The last couch, on the right, could only fit two people on it. They were all dark red and made from the softest flaffy wool. Next to the TV was a door that led to a big room that had a pool.

A couple feet behind the couches was the circular planning table, which had a bunch of little trinkets spread across a big world map. About fifteen feet diagonal of that was their gaming table, which had cards, poker chips, and various cans of alcohol spread on and around it. This table was about twenty feet away from the doors and the kitchen. To their left and to the right of the door was the small kitchen. Just about ten feet away from that was a long glass table where the group ate at. At the gaming table, three of their teammates, were sitting.

One was a silvered haired woman, about twenty five years of age; she wore a dark purple overcoat that went over her red under-armor. She also had a grey belt around her waist and red high heels, which gave her two to three more inches to her six foot figure. This woman was named Jane, or as everyone else calls her J, because when she was a Pokémon poacher she went by the name of Hunter J. Jane was arm wrestling with a silver haired man named Steven Stone.

Steven was a middle aged man around the age of thirty; he stood at 6ft. 5 and always wore a tux for some reason. His hair was slicked back to where it almost looked like a skarmory. He wore purple shoes to match the purple zigzags on his black tux. His red ascot or scarf or whatever that thing is reached down to just under his chest. The old champion was struggling to move the ex-hunter's arm.

Watching the two in amusement was a woman with purple hair that was wrapped into two buns. She wore a purple, black, and white dress that reached to her knees; she also wore white heels to bring her up two inches, putting her at 5'8".

Suddenly the hunter looked up as the trio entered the room.

"Oh, N is here," She said slamming Stevens arm on the table with ease.

"Ahh!" Steven yelped. "Gosh darn it! How do you do that?" He said rubbing his sore arm.

"What, you mean beating a weakling?" J said smirking back at him.

The ex-champion stood up angrily.

"Hey I'm not weak," He said as his face grew red with anger and embarrassment. "I'll have you know that I was Champion of Hoenn!"

"Then that doesn't make you strong, it makes your Pokémon strong." Jane said. "Took you long enough." She said turning her attention to N. "What took you so long?"

"Oh lover boy just got done with _quality_ time with Hilda." Mars said in a mocking tone as the three walked in the room.

N looked away, blushing.

"Okay, everyone ready?" Steven asked looking at his teammates.

Everyone nodded.

"OK then, let's go." He said walking to the door.

 **Scene Change** **-** **Hallway to Meeting point**

The group of six walked quickly down the damp cement hallway.

"What room was it again?" Mars said skipping next to J.

The silver haired woman sighed; this was the third time she asked. "It's room 1026 Mars. You would know if you would get your head out of your stupid computer." She said rolling her eyes.

"Hey! I was on level 26 of _Galaga_." Mars defended. "I was beating Saturn's high score."

"So that was _YOU_!?" Saturn said getting in the red head's face. "Do you know how long it took me to stay at the top?"

"Boo hoo, get over it." Jane said pushing his face out of the way. "Ash also announced it to us before he left."

Mars looked away blushing. "It was a good game."

"Sure it was."

The group continued walking down the hall chatting until they reached the steel door.

"Great!" Saturn said flailing his arms angrily. "How do we get in?"

"Hold on wimp." Mars said smugly as she walked past the fuming blue haired general.

She walked up to the steel plated door and started pushing on it with her shoulder. After a short while she stopped.

"Wow this is heavy." She said starting to push again. "Come on guys help me out here."

"Ha! Who's the weakling now?" Saturn asked mockingly to his red haired friend.

"Shut up and help me." Mars growled.

"Okay, okay." Saturn said walking next to her and pushing his hands against the door.

Both pushed as hard as they could but the door wouldn't budge.

"Argh!" Saturn groaned "This door ….is….really stuck….guys help us out."

N and Jupiter rolled their eyes and stepped up and started pushing….and pushing….and pushing….

Jane and Steven watched in amusement, but enough was enough.

"You guys are a bunch of idiots." Jane said as she walked beside the door and revealed a silver card slot.

The quad's eyes widened as she quickly slid her card in the slot and the light went from red to green and the door slid open.

"AHHH!" They screamed in a union as they all fell in a pile. Right in front of an angry looking commander.

He stood at 6ft. 8. He was wearing a black muscle shirt, which hugged his toned body tightly, under a dark green insolated vest. He was wearing a pair of dark blue jeans with a black belt that was laced with dark silver spuds wrapped around his waist. Around his neck was a green stone with a yellow circle that represented the head of Rayquaza it was kept in place by a dark silver dragon hand and a black string. His eyes were a golden hazel with a dark red around his pulps that change colors depending on the mood he was in. Under his eyes were two 'z's that were right above the scowl he had on his face.

All of them looked up fearfully at their leader.

"H-hey Ash," Mars stuttered as she pulled herself from the bottom of the pile and rolled on her back. "How was your morning?" She asked politely

"Oh it was fantastic; I mean there's nothing like waiting in a cold damp room for a team that likes to take their dear old time to get their rear ends down to meeting area." He said in a joyous tone. "How was your morning?"

"Really?" Mars asked confused on what to say.

"NO, NOT REALLY! HOW MANY TIMES HAVE I TOLD YOU NOT TO SHOW UP LATE?" He yelled angrily at them. "HOW MANY TIMES DOES IT TAKE TO GET THROUGH YOUR THICK SKULLS TO ACCUCUALLY SHOW UP EARLY AND PREPARE A HEAD OF TIME? NOW GET OFF YOUR SORRY BUTTS AND STAND AT ATTENTION UNTIL I COME UP WITH A PUNISHMENT FOR YOU SIX OR UNTIL YOU'RE TOLD OTHERWISE!"

Everyone cringed at the last sentence.

"Wait did I hear correctly?" Jane said walking in with Steven. "Did you say us six?"

"Did I stutter?" Neptune said glaring at the ex-hunter, earning another cringe from the group.

"W-well n-no Ash"

"No Ash that's right!" He barked. "Now all of you get up and get in line BEFORE I MAKE YOUR PUNISHMENT WORSE!"

Jane looked afraid as she rushed to get in line with everyone else.

"Yes sir!" the six said in a fearful union.

"Now," Cyrus said drawing everyone's attention. "As you know some of you'll be placed as spies in the Team Magma and Team Aqua bases."

We all nodded.

"Well," He continued. "They seem to be trying to make elite groups of their strongest members, much like you and Team Sapphire before they…well you know."

They all nodded again in reembrace of our fallen allies.

"So in order to find out who their strongest is they will be holding a tournament." Cyrus informed us. "And you will be entering those tournaments. Jane, Neptune, and Mars, you will be going to Team Magma. N, Steven both of you will be in Team Aqua. Your uniforms will be found in your rooms."

"Wait why?" N asked raising his hand.

"Why? What?"

"Why are we entering the tournament?"

"It's because the higher up we are, the closer we get to the leaders and the closer we get to the leaders the more information we get so it is easier to take down the powerhouse teams." Neptune said looking back to the group who nodded in understanding.

"Err yes that's right." Cyrus said nodding. "Jupiter, Saturn, you two will stay at home base. Now I understand it's not a lot of information and all of you need to get ready for your depart so prepare your Pokémon and make sure you go over your drop off plans to enter each of your designated teams so you are all dismissed and may Arceus be with you."

"Yes Sir!"

Scene Change: Hallway to Team Ruby Living Quarters

The group was silently walking back, exchanging nervous glances while their raven haired general walked slowly behind.

It didn't take long to reach our living quarters. When they got to the big double doors the group pulled to a halt. They all looked at Neptune nervously.

"W-well?" Steven spoke up, getting the attention of his leader.

"Well what?" He asked stupidly.

"What's t-the punishment?" N said jumping in to save his colleague.

"Oh, right," he sighed. "You know what? Your punishment is…that you have to spend the rest of the day with each other." He said this angrily before smiling.

They just stood there confused as the general walked past them and opened one of the doors.

"Well come on then," he said looking back, smiling, as he walked in.

Mars was the first to snap out of the confusion and followed him, with the others following after.

 **A/N: Hey guys, sorry I didn't upload when I said I would, I was having technical difficulties! Anyways, thanks for reading! Peace ;-)**


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